Bioinformatics Core Facility

  • Clinical research
  • Fundamentale Research
  • Genomics
Localization
Centre de Génomique Fonctionnelle Bordeaux
DEMANDE D'UTILISATION

Contact

Description

The  Bordeaux  Bioinformatics  Center  (CBiB)  is  a  Bioinformatics  Core  Facility  that is  designed  to  address  the  challenges of the genomic revolution through  our  bioinformatics  and computational biology services and research initiatives in the following ways:

  • Conducting collaborative research and providing bioinformatics solutions in cancer: the  CBiB provides  environment  for  conducting  collaborative  research and  services,  tools   development,  data  analysis,  database  design,  supports  grant  applications,  training,  licensing  of   specialized software, and help with computing capabilities.
  • Cancer bioinformatics infrastructure development: The  CBiB works  in  close  collaboration  with  the  Bordeaux  University  (and  in  particular,  the   Mésocentre Aquitain) at the regional level,  the Institut Francais de Bioinformatique at  the national   level and the ELIXIR at the European level to deploy adequate infrastructure solutions

See the pdf

Activity

Hosting and maintenance of public software and databases: • Hosting and maintenance of software and/or data request of users, the CBiB deploys programs or data protected by a secure access. These may include software that requires a license and cannot be made publicly available (e.g. CLC Workbench) or data that the providers do not wish to make public (ex: genome sequences under embargo). • Development, exploitation and maintenance of databases and innovative services or international scale: through its research activities or collaborations, the CBiB develops new resources, services or databases, which are made publicly available on its website. • Customized software development software development for cases that are not covered by publicly available tools. • Supervision the CBiB hosts and manages permanent and contractual engineering staff and/or post-docs who develop specialized information systems (e.g. pipelines for the NGS data processing) or participate in the data analysis and interpretation (e.g. annotation of SNPs). In these projects, the CBiB also provides computational and storage resources. • Hosting and training of users of bioinformatics programs and databases receives biologists who whish to master the use of bioinformatic tools. • Continued education M

Publication

  1. M. El-Kebir, H. Soueidan, T. Hume, D. Beisser, M. Dittrich, T. Müller, G. Blin, J. Hering, M. Nikolski, L. Wessels and G. Klau, xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model, Bioinformatics 2015, doi: 10.1093/bioinformatics/btv316
  2. N. Quenel-Tueux, M. Debled, J. Rudewicz, G. MacGrogan, M. Pulido, L. Mauriac, F. Dalenc, T. Bachelot, B. Lortal, C. Breton-Callu
  3. C. Tunon de Lara, M. Fournier, H. Bonnefoi, H. Soueidan, M. Nikolski, A. Gros, C. Daly, H. Wood, P. Rabbitts ans R. Iggo, Clinical and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in postmenopausal patients treated for large operable or locally advanced hormone-receptor-positive breast cancer, British Journal of Cancer 07/2015; DOI: 10.1038/ bjc.2015.247
  4. COSMOS Consortium COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access, Metabolomics Journal, 2015, doi: 10.1007/s11306-015-0810-y A. Sarkar and H. Soueidan and M. Nikolski, Identification of conserved gene clusters in multiple genomes based on synteny and homology, BMC Bioinformatics, vol 12 (Suppl 9), S18, 2011
  5. M. Cvijovic, H. Soueidan, D. Sherman, E. Klipp and M. Nikolski, Exploratory Simulation of Cell Ageing Using Hierarchical Models, Genome Informatics vol. 21, pp. 114-125, 2008

Collaboration

  • Mohammed El-Kebir, Brown University, Ben Raphael’s group, Providence, USA
  • Gunnar Klau, CWI Life Sciences, Algorithmic computational biology group, Amsterdam, Netherlands
  • Christoph Steinbeck, EBI, Cheminformatics and metabolism group, Wellcome Genome Campus, Hinxton, UK
  • Gabriele Valiente, Technical University of Catalonia, Barcelona, Spain
  • Lodweyk Wessels, The Netherlands Cancer Institute, Computational Cancer Biology, Amsterdam, Netherland